Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Host-specific fungal plant pathogens exhibit distinct interactions with the leaf microbiota of wild grasses.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026

Same author

Antimicrobial effectors of plant-associated fungi: multipurpose proteins with fast-evolving surfaces and structurally conserved cores.

Current opinion in microbiology·2026

Same author

Interspecies hybridization as a route of accessory chromosome origin in fungal pathogens.

mBio·2026

Same author

Polarising SNPs Without Outgroup.

Molecular ecology resources·2026

Same author

Genomic and physiological signatures of adaptation in pathogenic fungi.

Nature communications·2026

Same author

Limited directional selection but coevolutionary signals among imprinted genes in <i>A. lyrata</i>.

bioRxiv : the preprint server for biology·2025

Same journal

Genome-wide analysis across Indian camel populations reveals genetic distinctiveness of the Kharai camel breed.

BMC genomics·2026

Same journal

Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.

BMC genomics·2026

Same journal

From nurse bee to queen egg: RNA-seq analysis of Apis mellifera eggs shows dietary protein-dependent gene regulation.

BMC genomics·2026

Same journal

A genome-wide association study to identify the genetic loci underlying carbapenem resistance in Acinetobacter baumannii.

BMC genomics·2026

Same journal

Comparative transcriptome analysis to reveal key drought stress-responsive genes in sorghum (Sorghum bicolor (L.) Moench).

BMC genomics·2026

Same journal

Tissue identity is the dominant determinant of cross-species transferability of a porcine developmental programme.

BMC genomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 3, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

MafFilter: a highly flexible and extensible multiple genome alignment files processor.

Julien Y Dutheil¹, Sylvain Gaillard, Eva H Stukenbrock

¹Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany. julien.dutheil@mpi-marburg.mpg.de.

|January 23, 2014

Summary

This summary is machine-generated.

MafFilter is a C++ program that efficiently processes large genome alignments in Multiple Alignment Format (MAF) files. This tool facilitates custom data filtering and analysis pipelines for evolutionary and comparative genomics studies.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: May 3, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genome sequence alignments are crucial for evolutionary and comparative analyses.
Multiple Alignment Format (MAF) files store complex genomic alignment data, requiring efficient processing.
Analyzing large MAF files necessitates effective parsing and manipulation techniques.

Purpose of the Study:

To introduce MafFilter, a command-line C++ program for efficient processing of genome alignments.
To provide a flexible and extensible tool for manipulating Multiple Alignment Format (MAF) files.
To enable custom data filtering and analysis pipelines for genomic studies.

Main Methods:

Developed MafFilter as a command-line driven C++ program.
Implemented an extensive set of user-configurable tools within MafFilter.
Demonstrated functionality and performance using primate and fungal genomics data.

Main Results:

MafFilter efficiently processes genome alignments stored in MAF files.
The software supports window-based filtering, feature extraction, and statistical calculations.
Analyses included phylogenetics and population genomics on diverse biological datasets.

Conclusions:

MafFilter is a highly efficient and flexible tool for analyzing multiple genome alignments.
It enables the creation of custom data analysis pipelines by combining various methods.
MafFilter is an open-source software solution available for genomic research.